Question: Venn Diagramm or Alternative: Compare Protein Lists and add Annotation: Cellular Component
gravatar for Benni
3.8 years ago by
Benni30 wrote:

I want to compare protein lists (Uniprot Acc) in a Venn Diagramm or an alternative (Venn only works for max. 3 Lists?). Then I want to take the unique proteins for every list and make a cake diagramm of every list, which shows the distribution of the Cellular Component Annotation. Eg. The unique proteins in list 4 are 60% membrane associated.

Do you know a good tool for that?, a Tutorial? I would prefer: Python, Cytoscape, a Website, maybe Bioconductor?

UPDATE: I think I will use matplotlib-venn for the Venn Diagram. But how can I annotate the Protein lists with the GO Terms? I don´t want to be to specific with the Term, but also not to general. I can use to get a pie chart of my gene list with the Cellular Component Ontology. But half of the pie is then "cell part" which is to general. The childs are: intracellular (GO:0005622) and plasma membrane (GO:0005886). I want to distiguish between both components in the final pie chart. So is their a way to map GO Terms to a protein list with regard of the GO Term "depth"/"level"?

venn protein go annotation • 1.7k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Benni30

Not used it and not one of the tools you mentioned but looks promising

ADD REPLYlink written 3.8 years ago by microfuge1.6k

The package venneuler can take more than 3 lists.

ADD REPLYlink written 3.8 years ago by Jean-Karim Heriche22k
gravatar for WouterDeCoster
3.8 years ago by
WouterDeCoster43k wrote:

Have a look at this code I wrote some time ago: Executes as python file1 file2 [file3]

It will save a venn diagram of 2 or 3 sets and also open the plot. It will also write the sets to a file. Standard it assumes your file has no header, but with -h you can change this. With -names you can give names to your sets, but standard the file names are used for convenience. Handling arguments could have been better but well this works.

If you know a bit of python it is pretty straightforward to edit for your convenience ;-)

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by WouterDeCoster43k
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